Ligand profile

MGP

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_0068 — dATP pyrophosphohydrolase

Via homolog PDB 6scx UniProt Q9BQG2 Formula C₁₁H₁₉N₅O₁₄P₃⁺
Mol. weight 538.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MGP
PDB
6scx
UniProt (similar protein)
Q9BQG2
Target protein
VK055_0068

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 538.22 Da
LogP (Crippen) -2.91
H-bond donors 8
H-bond acceptors 13
TPSA 290.09 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.55
Formula C₁₁H₁₉N₅O₁₄P₃⁺

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 290.1
  • −1 ≤ LogP ≤ 5 -2.91
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 538.2
  • LogP ≤ 5 -2.91
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 290.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
InChI 
InChI=1S/C11H18N5O14P3/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(28-10)2-27-32(23,24)30-33(25,26)29-31(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H6-,12,13,14,19,20,21,22,23,24,25,26)/p+1/t4-,6-,7-,10-/m1/s1
InChIKey 
DKVRNHPCAOHRSI-KQYNXXCUSA-O

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00293

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0068.

PDB 2

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)